szhengczii
commented
4 months ago The command line has some mistakes and misses some parameters. AreTomo3 -InMdoc *./frames/.mdoc -OutDir test_Aretomo3 -PixSize 0.7894 -kV 300 -Cs 2.7 -Gpu 0 -AlignZ 800 -wbp -gain gain_ref.mrc -TotalDose 2.89** -VolZ 500 -McBin 4
The simplest command line in your case should look like below: AreTomo3 -InMdoc ./frames/ -InSuffix .mdoc -OutDir test_Aretomo3 -PixSize 0.7894 -kV 300 -Cs 2.7 -Gpu 0 -AlignZ 800 -wbp 1 -gain gain_ref.mrc -FmDose 2.89 -VolZ 800 -McBin 4 -Serial 1
The doc folder contains an user manual. Hope it can clarify a bit.
Sorry for the late response. Please report issues by email in the future. I do not check github on a regular base.
Best, Shawn
Hi, I try to run AreTomo3 but i get the following error during tomogram reconstruction: My command:
AreTomo3 -InMdoc ./frames/*.mdoc -OutDir test_Aretomo3 -PixSize 0.7894 -kV 300 -Cs 2.7 -Gpu 0 -AlignZ 800 -wbp -gain gain_ref.mrc -TotalDose 2.89 -VolZ 500 -McBin 4
The error': -InMdoc ./frames/TS_11.mrc.mdoc -InSuffix
-InSkips
-OutDir test_Aretomo3/ -TmpFile
-LogDir / -PixSize 0.79 -kV 300 -Cs 2.70 -FmDose 0.00000 -Serial 0 -Cmd 0 -Resume 0 -Gpu 0
Motion correction input parameters
-FmIntFile
-Gain gain_ref.mrc -Dark
-DefectFile
-EerSampling 1 -McPatch 0 0 0 -McIter 15 -McTol 0.10 -McBin 4.00 -Group 1 4 -FmRef -1 -RotGain 0 -FlipGain 0 -InvGain 0 -Mag 1.00 1.00 0.00 -InFmMotion 0 -TiffOrder 1 0
Tomography input parameters
-TotalDose 2.890000 -AlignZ 800 -VolZ 500 -AtBin 1.00 -TiltAxis 0.00 1.00 -TiltCor 0.00 0.00 -ReconRange -90.00 90.00 -AmpContrast 0.07 -ExtPhase 0.00 0.00 -FlipVol 0 -FlipInt 0 -Sart 20 5 -Wbp 0 -AtPatch 0 0 -OutXF 0 -Align 1 -CropVol 0 0 -OutImod 0 -DarkTol 0.70 -IntpCor 0 -CorrCTF 1 15
GPU 0 memory: 24249 MB
Load gain refereince from gain_ref.mrc Gain reference has been loaded.
All mdoc files have been processed, waiting processing to finish.
GPU 0: Motion correct 2Dvs3D_53-1100041-40.0_Jul31_17.19.55.tif
TIFF file size & mode: 5760 4092 3 0 Rendered size & mode: 5760 4092 3 0 GPU 0 Allocation time: GPU ( 0.26 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s GPU 0 Allocation time: GPU ( 0.35 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s GPU 0 Allocation time: GPU ( 0.07 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s GPU 0 Allocation time: GPU ( 0.26 GB) 0.00 s, CPU ( 0.00 GB) 0.00 s Create buffers: 0.10 seconds
Detect bad and hot pixels. Mean & Std: 0.00 0.00 Hot pixel threshold: 10.00
CC Mean Std: 0.000e+00 0.000e+00 CC threshold: 0.000
Full frame alignment Forward FFT of stack, please wait... Fourier transform done. Full-frame alignment has been started. Iteration 1 Error: 87.620 Iteration 2 Error: 87.620 Iteration 3 Error: 87.620 Iteration 4 Error: 87.620 Iteration 5 Error: 87.620 Iteration 6 Error: 87.620 Iteration 7 Error: 87.620 Iteration 8 Error: 87.620 Iteration 9 Error: 87.620 Iteration 10 Error: 87.620 Iteration 11 Error: 87.620 Iteration 12 Error: 87.620 Iteration 13 Error: 87.620 Iteration 14 Error: 87.620 Iteration 15 Error: 87.620
Full-frame alignment shift ...... Frame ( 1) shift: 0.000 0.000 ...... Frame ( 2) shift: 0.000 0.000 ...... Frame ( 3) shift: 0.000 0.000
Create aligned sum based upon full frame alignment. Mag stretch: 1.000 -0.000
CCufft2D::DestroyPlan:62: no kernel image is available for execution on the device
AreTomo3: MaUtil/CSimpleFuncs.cpp:49: void McAreTomo::MaUtil::CheckCudaError(const char*): Assertion `0' failed. Aborted (core dumped)
Any idea where the problem comes from ?
Many thanks for the help
Best,
Ramteen